AutoCloner

Multiple sequence alignment - TraesCS7A01G557900

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)

BLAST Results

Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

	qseqid	sseqid	percentage.identical	alignment.length	no.mismatch	no.gap.openings	qstart	qend	sstart	send	evalue	bitscore
0	TraesCS7A01G557900	chr7A	100.000	3017	0	0	1	3017	730503554	730506570	0.000000e+00	5572.0
1	TraesCS7A01G557900	chr7A	88.889	54	5	1	97	149	730529491	730529544	6.980000e-07	65.8
2	TraesCS7A01G557900	chr7D	92.294	2271	120	23	1	2231	635518913	635516658	0.000000e+00	3173.0
3	TraesCS7A01G557900	chr7D	89.176	425	32	11	2548	2962	49797705	49798125	4.460000e-143	518.0
4	TraesCS7A01G557900	chr7D	95.217	230	9	2	2225	2453	635516331	635516103	2.210000e-96	363.0
5	TraesCS7A01G557900	chr7D	90.686	204	17	2	1133	1334	635441219	635441016	1.380000e-68	270.0
6	TraesCS7A01G557900	chr7B	90.795	1510	107	15	3	1508	740237709	740239190	0.000000e+00	1989.0
7	TraesCS7A01G557900	chr7B	88.685	1414	108	23	96	1497	740722141	740723514	0.000000e+00	1677.0
8	TraesCS7A01G557900	chr7B	92.962	1023	67	4	1005	2026	740260991	740262009	0.000000e+00	1485.0
9	TraesCS7A01G557900	chr7B	87.413	1295	99	19	207	1497	740763141	740764375	0.000000e+00	1430.0
10	TraesCS7A01G557900	chr7B	90.367	872	43	16	1461	2292	740301807	740302677	0.000000e+00	1107.0
11	TraesCS7A01G557900	chr7B	92.135	623	40	6	1499	2113	740239657	740240278	0.000000e+00	870.0
12	TraesCS7A01G557900	chr7B	84.955	771	87	19	96	851	740300888	740301644	0.000000e+00	754.0
13	TraesCS7A01G557900	chr7B	91.977	349	24	3	2107	2453	740240306	740240652	1.260000e-133	486.0
14	TraesCS7A01G557900	chr7B	84.298	242	36	2	678	918	414077179	414077419	5.030000e-58	235.0
15	TraesCS7A01G557900	chr7B	93.269	104	7	0	2350	2453	740302677	740302780	1.450000e-33	154.0
16	TraesCS7A01G557900	chr1D	92.068	996	69	5	1031	2026	326909473	326908488	0.000000e+00	1393.0
17	TraesCS7A01G557900	chr1D	86.813	273	32	3	170	440	290446074	290446344	4.890000e-78	302.0
18	TraesCS7A01G557900	chr1D	83.041	342	32	11	2110	2448	326908428	326908110	1.370000e-73	287.0
19	TraesCS7A01G557900	chr1B	91.800	1000	71	6	1028	2026	441386183	441385194	0.000000e+00	1382.0
20	TraesCS7A01G557900	chr1B	91.295	471	26	7	2548	3017	185069472	185069016	1.970000e-176	628.0
21	TraesCS7A01G557900	chr1B	95.397	239	8	2	2782	3017	465361190	465360952	7.900000e-101	377.0
22	TraesCS7A01G557900	chr1A	91.420	1014	76	5	1005	2017	410155663	410156666	0.000000e+00	1380.0
23	TraesCS7A01G557900	chr1A	90.526	95	8	1	2454	2547	435729395	435729301	1.140000e-24	124.0
24	TraesCS7A01G557900	chr5B	96.391	471	15	2	2548	3017	230884339	230884808	0.000000e+00	774.0
25	TraesCS7A01G557900	chr5B	90.678	472	30	10	2548	3017	120307635	120308094	1.540000e-172	616.0
26	TraesCS7A01G557900	chr5B	84.310	478	54	18	2548	3017	507694251	507694715	5.930000e-122	448.0
27	TraesCS7A01G557900	chr2B	90.678	472	26	6	2548	3017	592558539	592558994	1.990000e-171	612.0
28	TraesCS7A01G557900	chr2B	82.231	242	39	4	679	918	557731909	557731670	3.940000e-49	206.0
29	TraesCS7A01G557900	chr2B	90.526	95	8	1	2454	2547	652507426	652507332	1.140000e-24	124.0
30	TraesCS7A01G557900	chr2B	89.474	95	9	1	2454	2547	356957757	356957663	5.280000e-23	119.0
31	TraesCS7A01G557900	chr5D	87.154	506	44	14	2530	3017	130453464	130453966	3.400000e-154	555.0
32	TraesCS7A01G557900	chr6B	88.372	473	21	11	2548	3017	220573504	220573063	3.420000e-149	538.0
33	TraesCS7A01G557900	chr6B	91.000	100	3	3	2454	2547	178270721	178270622	2.440000e-26	130.0
34	TraesCS7A01G557900	chr6B	90.526	95	8	1	2454	2547	623705034	623704940	1.140000e-24	124.0
35	TraesCS7A01G557900	chr3B	89.706	408	22	11	2611	3017	29347874	29348262	1.250000e-138	503.0
36	TraesCS7A01G557900	chr3B	84.384	365	35	16	2661	3014	420332270	420331917	3.730000e-89	339.0
37	TraesCS7A01G557900	chr3B	72.883	933	224	26	1100	2014	773542576	773543497	8.180000e-76	294.0
38	TraesCS7A01G557900	chr3B	72.647	903	220	23	1100	1985	771253096	771253988	1.070000e-69	274.0
39	TraesCS7A01G557900	chr3B	73.770	488	110	18	1546	2022	768341977	768342457	3.090000e-40	176.0
40	TraesCS7A01G557900	chr3B	76.707	249	51	5	1771	2014	771532786	771532540	6.790000e-27	132.0
41	TraesCS7A01G557900	chr3B	88.660	97	10	1	2452	2547	167241198	167241294	1.900000e-22	117.0
42	TraesCS7A01G557900	chr4A	85.339	457	40	17	2551	3001	739602262	739601827	5.930000e-122	448.0
43	TraesCS7A01G557900	chrUn	88.278	273	28	3	170	440	237218695	237218425	1.040000e-84	324.0
44	TraesCS7A01G557900	chr6A	87.179	273	31	3	170	440	105585603	105585873	1.050000e-79	307.0
45	TraesCS7A01G557900	chr6A	96.250	80	2	1	2469	2547	187129967	187129888	2.440000e-26	130.0
46	TraesCS7A01G557900	chr6A	89.583	96	7	3	2454	2547	158409049	158408955	5.280000e-23	119.0
47	TraesCS7A01G557900	chr2D	87.132	272	31	3	170	439	551888608	551888877	3.780000e-79	305.0
48	TraesCS7A01G557900	chr2D	86.813	273	32	3	169	439	482892497	482892767	4.890000e-78	302.0
49	TraesCS7A01G557900	chr2D	91.667	96	7	1	2453	2547	55359010	55359105	6.790000e-27	132.0
50	TraesCS7A01G557900	chr2A	86.989	269	32	2	173	440	156663809	156663543	1.760000e-77	300.0
51	TraesCS7A01G557900	chr3D	72.306	928	236	17	1100	2013	577657966	577657046	1.380000e-68	270.0
52	TraesCS7A01G557900	chr3D	73.552	397	94	9	1099	1487	579305634	579306027	1.130000e-29	141.0
53	TraesCS7A01G557900	chr3D	76.033	242	50	8	1711	1948	577789550	577789313	5.280000e-23	119.0
54	TraesCS7A01G557900	chr3D	78.443	167	29	7	1781	1944	577413984	577413822	5.320000e-18	102.0
55	TraesCS7A01G557900	chr3D	76.923	169	31	8	1781	1945	577383036	577383200	4.140000e-14	89.8
56	TraesCS7A01G557900	chr3D	77.922	154	25	8	1868	2015	437026278	437026128	1.490000e-13	87.9
57	TraesCS7A01G557900	chr3D	80.769	104	16	4	1847	1948	577969886	577969987	8.970000e-11	78.7
58	TraesCS7A01G557900	chr3D	74.850	167	26	11	1787	1945	577409845	577409687	9.030000e-06	62.1
59	TraesCS7A01G557900	chr3A	71.683	897	239	14	1100	1985	714535182	714536074	5.030000e-58	235.0
60	TraesCS7A01G557900	chr5A	82.231	242	39	4	680	919	515510813	515511052	3.940000e-49	206.0
61	TraesCS7A01G557900	chr5A	81.967	244	38	6	680	920	563840889	563841129	5.100000e-48	202.0

These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

	query	scaffold	start	end	length	rev.comp	avg.bitscore	max.bitscore	avg.percent.identical	query.start	query.end	num_hsp	groupid	homo_length
0	TraesCS7A01G557900	chr7A	730503554	730506570	3016	False	5572.000000	5572	100.000000	1	3017	1	chr7A.!!$F1	3016
1	TraesCS7A01G557900	chr7D	635516103	635518913	2810	True	1768.000000	3173	93.755500	1	2453	2	chr7D.!!$R2	2452
2	TraesCS7A01G557900	chr7B	740722141	740723514	1373	False	1677.000000	1677	88.685000	96	1497	1	chr7B.!!$F3	1401
3	TraesCS7A01G557900	chr7B	740260991	740262009	1018	False	1485.000000	1485	92.962000	1005	2026	1	chr7B.!!$F2	1021
4	TraesCS7A01G557900	chr7B	740763141	740764375	1234	False	1430.000000	1430	87.413000	207	1497	1	chr7B.!!$F4	1290
5	TraesCS7A01G557900	chr7B	740237709	740240652	2943	False	1115.000000	1989	91.635667	3	2453	3	chr7B.!!$F5	2450
6	TraesCS7A01G557900	chr7B	740300888	740302780	1892	False	671.666667	1107	89.530333	96	2453	3	chr7B.!!$F6	2357
7	TraesCS7A01G557900	chr1D	326908110	326909473	1363	True	840.000000	1393	87.554500	1031	2448	2	chr1D.!!$R1	1417
8	TraesCS7A01G557900	chr1B	441385194	441386183	989	True	1382.000000	1382	91.800000	1028	2026	1	chr1B.!!$R2	998
9	TraesCS7A01G557900	chr1A	410155663	410156666	1003	False	1380.000000	1380	91.420000	1005	2017	1	chr1A.!!$F1	1012
10	TraesCS7A01G557900	chr5D	130453464	130453966	502	False	555.000000	555	87.154000	2530	3017	1	chr5D.!!$F1	487
11	TraesCS7A01G557900	chr3B	773542576	773543497	921	False	294.000000	294	72.883000	1100	2014	1	chr3B.!!$F5	914
12	TraesCS7A01G557900	chr3B	771253096	771253988	892	False	274.000000	274	72.647000	1100	1985	1	chr3B.!!$F4	885
13	TraesCS7A01G557900	chr3D	577657046	577657966	920	True	270.000000	270	72.306000	1100	2013	1	chr3D.!!$R2	913
14	TraesCS7A01G557900	chr3A	714535182	714536074	892	False	235.000000	235	71.683000	1100	1985	1	chr3A.!!$F1	885

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
556	583	1.247567	CCTCGCCAACAGGTGAAAAT	58.752	50.0	0.0	0.0	41.15	1.82	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2529	3620	0.393537	CCTGTCCAGTCTTCATGGGC	60.394	60.0	0.0	0.0	43.02	5.36	R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
18	19	3.680842	CTATAACCCAGGTGTCGGC	57.319	57.895	0.00	0.00	0.00	5.54
149	150	5.350504	AGAGTATGTGGGTGAAAGAGATG	57.649	43.478	0.00	0.00	0.00	2.90
150	151	4.163078	AGAGTATGTGGGTGAAAGAGATGG	59.837	45.833	0.00	0.00	0.00	3.51
221	232	6.074648	TGAATTTTCCTTTAGAGCCCTTTGA	58.925	36.000	0.00	0.00	0.00	2.69
259	270	8.951243	GGATTCCTATTTCTACATAGAATTGGC	58.049	37.037	2.25	0.00	41.52	4.52
277	290	9.652114	AGAATTGGCTCCTATCTTTCATATTTT	57.348	29.630	0.00	0.00	0.00	1.82
303	316	8.650143	AAAGGAAAATAAACATGAGCCTAGAA	57.350	30.769	0.00	0.00	0.00	2.10
318	331	8.821686	TGAGCCTAGAATCAATGGAAAAATTA	57.178	30.769	0.00	0.00	0.00	1.40
556	583	1.247567	CCTCGCCAACAGGTGAAAAT	58.752	50.000	0.00	0.00	41.15	1.82
563	590	2.557924	CCAACAGGTGAAAATGCTGCTA	59.442	45.455	0.00	0.00	0.00	3.49
601	628	4.548451	TCATGCATTGCCACCATTTTTA	57.452	36.364	6.12	0.00	0.00	1.52
643	677	4.764308	TGCATTGCCGCCATTATATTCTTA	59.236	37.500	6.12	0.00	0.00	2.10
703	737	6.295719	ACTACCTTCGTCCTGATTTATTGT	57.704	37.500	0.00	0.00	0.00	2.71
711	745	5.045869	TCGTCCTGATTTATTGTCCTCCTTT	60.046	40.000	0.00	0.00	0.00	3.11
770	805	8.987890	ACTAAACAAATTTTGATGCATGTAACC	58.012	29.630	15.81	0.00	0.00	2.85
774	809	7.863666	ACAAATTTTGATGCATGTAACCAAAG	58.136	30.769	15.81	0.00	0.00	2.77
775	810	7.498570	ACAAATTTTGATGCATGTAACCAAAGT	59.501	29.630	15.81	1.81	0.00	2.66
847	882	8.770438	ATTTGGTGACACGCATTATAATTTTT	57.230	26.923	0.00	0.00	42.67	1.94
956	1109	5.047021	ACATATCATTTCGGATCGATGTCCT	60.047	40.000	0.54	0.00	35.23	3.85
975	1128	1.833630	CTGACACTGATAGGGAAGCCA	59.166	52.381	0.00	0.00	0.00	4.75
1047	1200	7.514721	ACAGGTTATTTTCTCAGAGGTTAACA	58.485	34.615	8.10	0.00	0.00	2.41
1726	2372	2.094906	CAGAACCTGTTCGATACCACGA	60.095	50.000	4.49	0.00	43.97	4.35
2026	2672	1.824852	TCAACTTCTGATGGCGCTAGA	59.175	47.619	7.64	3.65	0.00	2.43
2042	2695	8.220755	TGGCGCTAGATATTCTTTTAACAATT	57.779	30.769	7.64	0.00	0.00	2.32
2064	2717	1.922570	AGTTGCTTACATACGCGAGG	58.077	50.000	15.93	3.63	0.00	4.63
2130	2832	2.915463	GAGCGTGTATGCCATACGTATC	59.085	50.000	4.74	0.00	43.07	2.24
2133	2835	3.242518	CGTGTATGCCATACGTATCTGG	58.757	50.000	4.74	8.01	38.59	3.86
2285	3320	1.914634	AGCAGATGTAAACGCTCTCG	58.085	50.000	0.00	0.00	42.43	4.04
2454	3545	7.953005	TCCTATATTTTTGAAATGCTCACCA	57.047	32.000	0.00	0.00	32.21	4.17
2455	3546	7.999679	TCCTATATTTTTGAAATGCTCACCAG	58.000	34.615	0.00	0.00	32.21	4.00
2456	3547	7.068593	TCCTATATTTTTGAAATGCTCACCAGG	59.931	37.037	0.00	0.00	32.21	4.45
2457	3548	3.749665	TTTTTGAAATGCTCACCAGGG	57.250	42.857	0.00	0.00	32.21	4.45
2458	3549	1.631405	TTTGAAATGCTCACCAGGGG	58.369	50.000	0.00	0.00	32.21	4.79
2459	3550	0.899717	TTGAAATGCTCACCAGGGGC	60.900	55.000	0.00	0.00	32.21	5.80
2460	3551	2.361610	AAATGCTCACCAGGGGCG	60.362	61.111	0.00	0.00	0.00	6.13
2461	3552	2.819984	GAAATGCTCACCAGGGGCGA	62.820	60.000	0.00	0.00	0.00	5.54
2462	3553	2.826777	AAATGCTCACCAGGGGCGAG	62.827	60.000	0.00	0.00	0.00	5.03
2482	3573	4.954970	CACGTTGGCCCAGCAGGT	62.955	66.667	0.00	0.00	38.26	4.00
2483	3574	3.246112	ACGTTGGCCCAGCAGGTA	61.246	61.111	0.00	0.00	38.26	3.08
2484	3575	2.436646	CGTTGGCCCAGCAGGTAG	60.437	66.667	0.00	0.00	38.26	3.18
2485	3576	2.751837	GTTGGCCCAGCAGGTAGC	60.752	66.667	0.00	0.00	46.19	3.58
2494	3585	4.225497	GCAGGTAGCCCATGACAC	57.775	61.111	0.00	0.00	37.23	3.67
2495	3586	1.452108	GCAGGTAGCCCATGACACC	60.452	63.158	0.00	0.00	37.23	4.16
2496	3587	1.153369	CAGGTAGCCCATGACACCG	60.153	63.158	0.00	0.00	36.14	4.94
2497	3588	2.189521	GGTAGCCCATGACACCGG	59.810	66.667	0.00	0.00	0.00	5.28
2498	3589	2.189521	GTAGCCCATGACACCGGG	59.810	66.667	6.32	7.33	46.15	5.73
2499	3590	2.285069	TAGCCCATGACACCGGGT	60.285	61.111	6.32	0.00	45.07	5.28
2500	3591	1.001888	TAGCCCATGACACCGGGTA	59.998	57.895	6.32	5.72	45.07	3.69
2501	3592	0.618107	TAGCCCATGACACCGGGTAA	60.618	55.000	6.32	0.00	45.07	2.85
2502	3593	1.001887	GCCCATGACACCGGGTAAA	60.002	57.895	6.32	0.00	45.07	2.01
2503	3594	0.609681	GCCCATGACACCGGGTAAAA	60.610	55.000	6.32	0.00	45.07	1.52
2504	3595	1.912417	CCCATGACACCGGGTAAAAA	58.088	50.000	6.32	0.00	37.70	1.94
2536	3627	9.555411	TTTACCTTATATATACAGAGCCCATGA	57.445	33.333	0.00	0.00	0.00	3.07
2537	3628	9.555411	TTACCTTATATATACAGAGCCCATGAA	57.445	33.333	0.00	0.00	0.00	2.57
2538	3629	8.083828	ACCTTATATATACAGAGCCCATGAAG	57.916	38.462	0.00	0.00	0.00	3.02
2539	3630	7.901322	ACCTTATATATACAGAGCCCATGAAGA	59.099	37.037	0.00	0.00	0.00	2.87
2540	3631	8.200792	CCTTATATATACAGAGCCCATGAAGAC	58.799	40.741	0.00	0.00	0.00	3.01
2541	3632	8.901472	TTATATATACAGAGCCCATGAAGACT	57.099	34.615	0.00	0.00	0.00	3.24
2542	3633	3.834489	ATACAGAGCCCATGAAGACTG	57.166	47.619	0.00	1.44	0.00	3.51
2543	3634	0.617413	ACAGAGCCCATGAAGACTGG	59.383	55.000	0.00	0.00	0.00	4.00
2544	3635	0.907486	CAGAGCCCATGAAGACTGGA	59.093	55.000	0.00	0.00	35.70	3.86
2545	3636	0.908198	AGAGCCCATGAAGACTGGAC	59.092	55.000	0.00	0.00	35.70	4.02
2546	3637	0.615331	GAGCCCATGAAGACTGGACA	59.385	55.000	0.00	0.00	35.70	4.02
2547	3638	0.617413	AGCCCATGAAGACTGGACAG	59.383	55.000	0.00	0.00	35.70	3.51
2614	3708	3.438360	CATAAAAGCTGGCGATCAAACC	58.562	45.455	0.00	0.00	0.00	3.27
2640	3734	2.274104	GGCCGGCCCATTTACAGA	59.726	61.111	36.64	0.00	0.00	3.41
2650	3744	2.482721	CCCATTTACAGAGTTCGCGTTT	59.517	45.455	5.77	0.00	0.00	3.60
2684	3778	1.825474	TCTTCTAGAGTTTCCCAGCCG	59.175	52.381	0.00	0.00	0.00	5.52
2685	3779	0.902531	TTCTAGAGTTTCCCAGCCGG	59.097	55.000	0.00	0.00	0.00	6.13
2712	3808	7.745620	TTTTCTAGTTTTGGGAAGCTTCTAG	57.254	36.000	25.05	16.25	0.00	2.43
2822	3921	8.460831	TCTTTTTCTTTTCCTTTTCTGTTTCG	57.539	30.769	0.00	0.00	0.00	3.46
2928	4036	6.702716	TCCCACTTTTAGAAACGTTCATTT	57.297	33.333	0.00	0.00	0.00	2.32

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
49	50	9.657419	CATAGTTATTTCCTTTCAAGCCATTTT	57.343	29.630	0.00	0.00	0.00	1.82
144	145	1.342374	ACCAAAAGGATGCCCCATCTC	60.342	52.381	5.32	0.00	40.39	2.75
149	150	1.347062	TCAAACCAAAAGGATGCCCC	58.653	50.000	0.00	0.00	0.00	5.80
150	151	2.289631	CCTTCAAACCAAAAGGATGCCC	60.290	50.000	0.00	0.00	44.02	5.36
197	204	6.074648	TCAAAGGGCTCTAAAGGAAAATTCA	58.925	36.000	0.00	0.00	0.00	2.57
277	290	9.747898	TTCTAGGCTCATGTTTATTTTCCTTTA	57.252	29.630	0.00	0.00	0.00	1.85
318	331	7.707624	AATGTCATTTGGTTCACATCATAGT	57.292	32.000	0.00	0.00	0.00	2.12
417	443	8.752005	TCTTTTTGGTTCATAGGATAGGATTG	57.248	34.615	0.00	0.00	28.27	2.67
451	477	5.841957	AGCTTCTAGGTTTGCATAATTGG	57.158	39.130	0.00	0.00	0.00	3.16
563	590	0.461870	TGAACACACAGCAAGCGAGT	60.462	50.000	0.00	0.00	0.00	4.18
643	677	0.104304	CGCCGTTAGATGCCCTAAGT	59.896	55.000	0.00	0.00	37.98	2.24
956	1109	1.951209	TGGCTTCCCTATCAGTGTCA	58.049	50.000	0.00	0.00	0.00	3.58
975	1128	4.860802	TGAGGTATGTGATTGGATGGTT	57.139	40.909	0.00	0.00	0.00	3.67
1227	1387	3.387091	ACGTAGATGCCCGTGCCA	61.387	61.111	0.00	0.00	35.69	4.92
1719	2365	0.968901	AGAAGGCGTCCATCGTGGTA	60.969	55.000	0.00	0.00	39.03	3.25
1726	2372	1.515954	CCGTGTAGAAGGCGTCCAT	59.484	57.895	0.00	0.00	0.00	3.41
2042	2695	2.921121	CTCGCGTATGTAAGCAACTTCA	59.079	45.455	5.77	0.00	0.00	3.02
2064	2717	1.131126	CGTTCATTGGGTGAGTGCATC	59.869	52.381	0.00	0.00	38.29	3.91
2067	2720	1.210155	GCGTTCATTGGGTGAGTGC	59.790	57.895	0.00	0.00	38.29	4.40
2095	2749	2.109480	ACACGCTCATAGGGATAGGGTA	59.891	50.000	0.00	0.00	34.97	3.69
2130	2832	9.440773	ACTGCACAATATATACATAATGTCCAG	57.559	33.333	0.00	0.00	40.19	3.86
2133	2835	7.899841	CGCACTGCACAATATATACATAATGTC	59.100	37.037	1.11	0.00	29.92	3.06
2208	2910	9.811995	TTGTATTAGTATAGCAAACCACTAGTG	57.188	33.333	16.34	16.34	0.00	2.74
2285	3320	9.539825	AATGTATGATCAATATATCGAGGAAGC	57.460	33.333	0.00	0.00	0.00	3.86
2465	3556	3.545124	TACCTGCTGGGCCAACGTG	62.545	63.158	14.82	0.27	39.10	4.49
2466	3557	3.246112	TACCTGCTGGGCCAACGT	61.246	61.111	14.82	3.62	39.10	3.99
2467	3558	2.436646	CTACCTGCTGGGCCAACG	60.437	66.667	14.82	0.00	39.10	4.10
2468	3559	2.751837	GCTACCTGCTGGGCCAAC	60.752	66.667	14.82	3.02	39.10	3.77
2469	3560	4.047125	GGCTACCTGCTGGGCCAA	62.047	66.667	20.33	0.00	39.52	4.52
2472	3563	3.813724	ATGGGCTACCTGCTGGGC	61.814	66.667	14.82	8.37	42.39	5.36
2473	3564	2.194056	CATGGGCTACCTGCTGGG	59.806	66.667	14.82	4.64	42.39	4.45
2474	3565	1.153086	GTCATGGGCTACCTGCTGG	60.153	63.158	8.29	8.29	42.39	4.85
2475	3566	0.745845	GTGTCATGGGCTACCTGCTG	60.746	60.000	0.00	0.00	42.39	4.41
2476	3567	1.604378	GTGTCATGGGCTACCTGCT	59.396	57.895	0.00	0.00	42.39	4.24
2477	3568	1.452108	GGTGTCATGGGCTACCTGC	60.452	63.158	0.00	0.00	41.94	4.85
2478	3569	1.153369	CGGTGTCATGGGCTACCTG	60.153	63.158	0.00	0.00	37.76	4.00
2479	3570	2.367202	CCGGTGTCATGGGCTACCT	61.367	63.158	0.00	0.00	37.76	3.08
2480	3571	2.189521	CCGGTGTCATGGGCTACC	59.810	66.667	0.00	0.00	37.24	3.18
2481	3572	2.189521	CCCGGTGTCATGGGCTAC	59.810	66.667	0.00	0.00	38.90	3.58
2510	3601	9.555411	TCATGGGCTCTGTATATATAAGGTAAA	57.445	33.333	0.00	0.00	0.00	2.01
2511	3602	9.555411	TTCATGGGCTCTGTATATATAAGGTAA	57.445	33.333	0.00	0.00	0.00	2.85
2512	3603	9.201989	CTTCATGGGCTCTGTATATATAAGGTA	57.798	37.037	0.00	0.00	0.00	3.08
2513	3604	7.901322	TCTTCATGGGCTCTGTATATATAAGGT	59.099	37.037	0.00	0.00	0.00	3.50
2514	3605	8.200792	GTCTTCATGGGCTCTGTATATATAAGG	58.799	40.741	0.00	0.00	0.00	2.69
2515	3606	8.976353	AGTCTTCATGGGCTCTGTATATATAAG	58.024	37.037	0.00	0.00	0.00	1.73
2516	3607	8.753133	CAGTCTTCATGGGCTCTGTATATATAA	58.247	37.037	0.00	0.00	0.00	0.98
2517	3608	7.343057	CCAGTCTTCATGGGCTCTGTATATATA	59.657	40.741	0.00	0.00	33.94	0.86
2518	3609	6.155910	CCAGTCTTCATGGGCTCTGTATATAT	59.844	42.308	0.00	0.00	33.94	0.86
2519	3610	5.481824	CCAGTCTTCATGGGCTCTGTATATA	59.518	44.000	0.00	0.00	33.94	0.86
2520	3611	4.285517	CCAGTCTTCATGGGCTCTGTATAT	59.714	45.833	0.00	0.00	33.94	0.86
2521	3612	3.643320	CCAGTCTTCATGGGCTCTGTATA	59.357	47.826	0.00	0.00	33.94	1.47
2522	3613	2.437281	CCAGTCTTCATGGGCTCTGTAT	59.563	50.000	0.00	0.00	33.94	2.29
2523	3614	1.833630	CCAGTCTTCATGGGCTCTGTA	59.166	52.381	0.00	0.00	33.94	2.74
2524	3615	0.617413	CCAGTCTTCATGGGCTCTGT	59.383	55.000	0.00	0.00	33.94	3.41
2525	3616	0.907486	TCCAGTCTTCATGGGCTCTG	59.093	55.000	0.00	0.00	38.44	3.35
2526	3617	0.908198	GTCCAGTCTTCATGGGCTCT	59.092	55.000	0.00	0.00	39.44	4.09
2527	3618	0.615331	TGTCCAGTCTTCATGGGCTC	59.385	55.000	0.00	0.00	43.13	4.70
2528	3619	0.617413	CTGTCCAGTCTTCATGGGCT	59.383	55.000	0.00	0.00	43.13	5.19
2529	3620	0.393537	CCTGTCCAGTCTTCATGGGC	60.394	60.000	0.00	0.00	43.02	5.36
2530	3621	1.279496	TCCTGTCCAGTCTTCATGGG	58.721	55.000	0.00	0.00	38.44	4.00
2531	3622	3.641434	ATTCCTGTCCAGTCTTCATGG	57.359	47.619	0.00	0.00	39.33	3.66
2532	3623	5.303971	GGATATTCCTGTCCAGTCTTCATG	58.696	45.833	0.00	0.00	33.05	3.07
2533	3624	5.559148	GGATATTCCTGTCCAGTCTTCAT	57.441	43.478	0.00	0.00	33.05	2.57
2547	3638	5.866633	CAGAGAGCGTCAAATAGGATATTCC	59.133	44.000	0.00	0.00	36.58	3.01
2610	3704	2.593436	CGGCCCAGTTCACGGTTT	60.593	61.111	0.00	0.00	0.00	3.27
2650	3744	3.841845	TCTAGAAGATTCCCAAAACCGGA	59.158	43.478	9.46	0.00	0.00	5.14
2694	3790	4.104897	ACCTTCTAGAAGCTTCCCAAAACT	59.895	41.667	24.58	5.11	37.11	2.66
2799	3898	8.596271	AACGAAACAGAAAAGGAAAAGAAAAA	57.404	26.923	0.00	0.00	0.00	1.94
2928	4036	5.932303	TGGAAAACACGACCATTTTTGAAAA	59.068	32.000	0.00	0.00	0.00	2.29
2932	4040	5.786401	TTTGGAAAACACGACCATTTTTG	57.214	34.783	0.00	0.00	33.56	2.44
2938	4046	4.457834	ACAATTTTGGAAAACACGACCA	57.542	36.364	0.00	0.00	0.00	4.02
2939	4047	4.865365	TGAACAATTTTGGAAAACACGACC	59.135	37.500	0.00	0.00	0.00	4.79

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.